1. EMERGING ISSUES IN MICROBIAL DIVERSITY SALT LAKE CITY, MAY 2002 WE TEACH MICROBIOLOGY BUT WE LEARN FROM MICROBES

2. SOME PERTINENT COMMENTS "the microbe always has the last word" "all life in the biosphere depends on microbes" "all microbiology is environmental microbiology"

3. THE HIDDEN WORLDS OF MICROBIOLOGY The number of prokaryote cells in the biosphere (but not the universe?) is estimated to be 6,000,000,000,000,000,000,000,000,000,000 (6 x 10 30 ). These contain 50% of the earth's carbon, 90% of nitrogen and phosphorus, and more than 10 8 species. In our colons, there are about 10 12 bacteria, not all of which have been identified. To date, only 1,500 microbes are known to cause disease in humans or animals. There are <10 9 bacteria in 1 gram of soil. A gram of soil contains 1,000-5,000 different species of bacteria. But what of the eukaryotic microbes? Recent studies show a vast hidden diversity of fungi and protists in the biosphere.

4. SOME APPLICATIONS BIOREMEDIATION FACTORIES ENZYMES, VECTORS, PROCESSES (PCR) DISEASE BIOTERRORISM FOOD AND FUEL DRUGS EVOLUTION MICROBES

5. WHY STUDY? The Limits of Life Diversity Cellular Interactions and Communities Evolution Disease Microbial Physiology Biotechnology and Bioterrorism

6. LIMITS OF LIFE Temperature: 4-130? pH: 1-10? Genetic: 20-78% G+C Pressure Chemical and physical stress

7. An example of microbes growing under stress: lichens in an extreme environment. Notre Dame, Paris.

8. DIVERSITY Microbial ecology of biological niches Metagenomes Unidentified microbial divisions Small eukaryotes Unrealised potential

9. DIRT TO PAYDIRT DIRT MICROBESAPPLICATIONSIDENTIFICATION (BIOCATALYSIS, BIOTRANSFORMATION) (MICROBIAL CATALOGUE) DNA rDNA SEQUENCE CATALOGUE METAGENOME GENES & PATHWAYS

10. INTERACTIONS Symbiosis Antagonism Commensalism Do all of these responses happen in microbial communities?

13. THE ROLES OF MICROBES IN THE EVOLUTION OF HIGHER LIFE FORMS AND THE CONSTANT EVOLUTION OF MICROBES : Morphogenesis Developmental programmes Regulatory networks Pathogenesis Why worry about life in space (astrobiology, etc.) when terrestrial microbes can provide clues as to the origins and evolution of eukaryotic differentiation?

14. A bacterial mouth!!? (Momma et al. J. Bact. 2000)

15. HORIZONTAL (LATERAL) GENE TRANSFER HOW CAN IT BE ESTABLISHED? 1. Demonstration in the laboratory or the environment 2. Sequence or motif similarity (DNA or protein) 3. Islands of distinct base composition 4. Nucleic acid hybridisation 5. Association with movable elements 6. Extrachromosomal association 7. Phenotypic and behavioral similarities

16. Disease Pathogenesis Prevention Treatment and Resistance

18. Know the enemy Life cycle and ecology of infectious microbes Evolutionary lineage Environmental changes associated with infection Host-range variation Diagnosis Mechanisms of host/pathogen interaction Mechanisms of resistance Host susceptibility determinants CELLULAR MICROBIOLOGY!

19. Cellular microbiology: the interaction of prokaryotes and eukaryotes

20. ANTIBIOTIC RESISTANCE MECHANISMS 2001 Decreased influx* Increased efflux* Enzymatic inactivation* Sequestration* Target modification* Target by-pass* Target repair Target amplification Biofilm formation ? Intracellular localisation *can be acquired by horizontal gene transfer From where? THAT IS THE QUESTION!

21. Aspects of Antibiotic Resistance The clinical problem (Medicine) Why it happened (Human nature) How it happened (Genetics) Mechanisms (Biochemistry) Origins (Speculation) Solutions (Politics)

22. HOW BUGS BECOME ANTIBIOTIC RESISTANT: THE PATHWAY TO BECOMING UNTREATABLE SENSITIVE MULTIDRUG RESISTANCE RESISTANCE (low) M (?) INCREASING SELECTION, STRESS, HYPERMUTATION RESISTANCE (medium)(compensation) MA RESISTANCE (high)(compensation) (antagonism)

25. LARGE IS SPECTACULAR, BUT SMALL IS BEAUTIFUL, TOO! Tantalus Range, B.C.

26. Genomes, GCs and Small Molecules Mycoplasma Chlamydia Neisseria Staphylococcus Mycobacteria Escherichia Pseudomonas Streptomycetes 52 37 66 50 67 75 Genome Size (Mb) SPECIALISTS GENERALISTS 846 2 Secondary Metabolite Production (%G+C) 42 40

27. MULTIPLE ACTIVITIES FOR SMALL MOLECULES IN BIOLOGY Growth inhibitors, allosteric effectors, transcription activators, pheromones, quorum sensors, insecticides, immunosuppressives, cell-signalling, hormone analogs, plant growth regulators, surfactants, antivirals, antitumour agents, herbicides, antiparasitics, antihelminthics, antifungals, cholesterol-lowering agents, and enzyme inhibitors

28. Signaling molecule diversity (I) O O H N H OOH O O Br Br Br AgrD1 thiolactone signaling peptide from Staphylococcus aureus Bacillus subtilis CSF (ERGMT) V. harveyi N-( -hydroxy-butyryl)- L-homoserine lactone Inhibitory furanone from marine algae Delisea pulchra OHO OCH 3 3-hydroxypalmitic acid ester from Ralstonia solanacearum

29. Signaling molecule diversity (II) O O H H N OO O O H N H O N O OH H N-(3-oxo-dodecanoyl)-L- homoserine lactone (PAI-1) N-butyryl homoserine lactone (PAI-2) 2-hydroxy-3 heptyl-4-quinolone (PQS) NH NH O O HH H N NH O O H H OH cyclo ( Ala-L-Val) cyclo (L-Pro-L-Tyr) from Pseudomonas aeruginosa: Cyclic dipeptides

30. ANTIBIOTICS Selection Induced mutagenesis Mutagenicity Transposition BiofilmsGene delivery Virulence Gene transfer Phage induction Role of antibiotics in the development of resistance

31. Biology is much more than DNA, RNA, proteins and membranes!

32. Perlman's rules (1980) always right your friend a sensitive partner The microorganism is There are NO stupid microorganisms. can Microorganisms do anything. will smarter thanchemists, Microorganisms arewiser thanengineers, more energetic thanetc. If you take care of your microbial friends, they will take care of your future and you will live happily ever after.

33. "It is essential that microbiology be perceived and practiced in a way consistent with the natural order of things; microbes are the base for and sustain all other life on this planet. Let us reorganize all of biology around microbiology." Carl R. Woese 1994

34. The genealogy of 'omic' sciences (or everyone wants their own "-omic") GENOMICS FUNCTIONAL GENOMICS GNOMICSMETAGENOMICS ENTEROMICSVIROMICS METABOLOMICS PHYSIOMICS PROTEOMICS RNOMICS ARRAYOMICS (TRANSCRIPTOMICS) ARCHEOMICS TRANSPOSOMICS BIOGEOMICS SYSTOMICS GLYCOMICS